As a key attribute of soil quality, soil organic matter (SOM) and its different fractions play an important role in regulating soil nutrient cycling and soil properties.This study evaluated the soil carbon (C) and nitrogen (N) concentrations in different SOM fractions (light– and heavy fractions, microbial biomass) under different vegetation types and analyzed their influencing factors in continuous permafrost regions along the Qinghai-Tibet Highway in the North of Kunlun Mountains, China. Soil samples were collected in pits under four vegetation types — Alpine swamp meadow (ASM), Alpine meadow (AM), Alpine steppe (AS) and Alpine desert (AD) — at the depth of 0-50 cm. The vegetation coverage was the highest at ASM and AM, followed by AS and AD. The results indicated that the concentrations of light fraction carbon (LFC) and nitrogen (LFN), and microbial biomass carbon (MBC) and nitrogen (MBN) decreased as follows: ASM > AM > AS > AD, with the relatively stronger decrease of LFC, whereas the heavy fraction carbon (HFC) and nitrogen (HFN) concentrations were lower in AS soils than in the AD soils. The relatively higher proportions of LFC/SOC and MBC/SOC in the 0-10 cm depth under the ASM soils are mainly resulted from its higher substrate input and soil moisture content. Correlation analysis demonstrated that aboveground biomass, soil moisture content, soil organic carbon (SOC) and total nitrogen (TN) positively correlated to LFC, LFN, HFC, HFN, MBC and MBN, while pH negatively correlated to LFC, LFN, HFC, HFN, MBC and MBN. There was no relationship between active layer thickness and SOM fractions, except for the LFC. Results suggested that vegetation cover, soil moisture content, and SOC and TN concentrations were significantly correlated with the amount and availability of SOM fractions, while permafrost had less impact on SOM fractions in permafrost regions of the central Qinghai–Tibet Plateau.